User:Susana Retamal/Sandbox1
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Background Information
Evidence of Fnr-Crp protein Involvement in Transcriptional Response to NaCl
Physico - Chemical parameters for Rsp1275
Amino Acid Conservation Scores
References
Background InformationBackground Information
Rsp1275 is a member of the Fnr-Crp family of transcriptional regulators. Homologues of the Fnr protein from E. coli have been identified in a variety of taxonomically diverse bacterial species. The bacterium Rhodobacter spheroides 2.4.1 encodes 8 members of this family, however only 2 have known function. The modeling of 7 of them were successfully obtained using 3D-Jigsaw, all being very similar in structure to Crp (the only one with crystal structure solved). The DNA binding domain helix-turn-helix is located in the C-terminal, and the N-terminal part contains the allosteric effector domain. Rsp1275 has been linked with salt-tolerance in Rhodobacter spheroides. Different genes coding for the Fnr-Crp proteins of unknown function have been cloned and a multicopy test was performed to evaluate these as potential regulators of NaCl-responsive genes.
Structure of the Proposed rsp1275'
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Evidence of Fnr-Crp protein Involvement in Transcriptional Response to NaClEvidence of Fnr-Crp protein Involvement in Transcriptional Response to NaCl
It has been proposed that Fnr-Crp protein encoded by rsp1275 is a transcription factor responsible for salt-responsive changes in the transcriptome. In addition, it's likely that rsp1275 interacts with a small ligand (potentially Na or Cl).
Physico - Chemical parameters for Rsp1275Physico - Chemical parameters for Rsp1275
Number of amino acids: 249
Molecular weight: 28014.2
Theoretical pI: 6.10
Globe Prediction: it appears as compact, as a globular domain.
Secondary Structure: Helix 34.94% Extended (sheet) 17.67% Loop 47.39%
| Amino Acid | Number present | Percentage of total present |
|---|---|---|
| Ala (A) | 15 | 8.8% |
| Arg (R) | 10 | 10.4% |
| Asn (N) | 6 | 2.4% |
| Asp (D) | 10 | 4.8% |
| Cys (C) | 1 | 1.2% |
| Gln (Q) | 5 | 2.8% |
| Glu (E) | 11 | 8.0% |
| Gly (G) | 9 | 7.6% |
| His (H) | 10 | 2.4% |
| Ile (I) | 3 | 4.0% |
| Leu (L) | 21 | 14.5% |
| Lys (K) | 6 | 1.2% |
| Met (M) | 6 | 2.4% |
| Phe (F) | 2 | 4.0% |
| Pro (P) | 8 | 5.2% |
| Ser (S) | 7 | 4.4% |
| Thr (T) | 13 | 6.4% |
| Trp (W) | 2 | 2.0% |
| Tyr (Y) | 6 | 0.4% |
| Val (V) | 12 | 5.6% |
| Pyl (O) | 0 | 0.% |
| Sec (U) | 0 | 0.0% |
Amino Acid Conservation ScoresAmino Acid Conservation Scores
- POS: The position of the AA in the SEQRES derived sequence. - SEQ: The SEQRES derived sequence in one letter code. - 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier. - SCORE: The normalized conservation scores. - COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable). - CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores. - CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval. - MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position. - RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.
POS SEQ 3LATOM SCORE COLOR CONFIDENCE INTERVAL CONFIDENCE INTERVAL COLORS MSA DATA RESIDUE VARIETY (normalized) 1 P PRO47: -1.063 8* -1.567,-0.697 9,7 3/19 P 2 G GLY48: -0.916 8 -1.417,-0.529 9,7 13/19 G,K 3 V VAL49: 1.226 2 0.404, 2.816 4,1 13/19 C,E,Q,R,V 4 T THR50: 1.816 1 0.790, 2.816 3,1 14/19 A,E,Q,T 5 L LEU51: 0.649 3* -0.136, 1.367 5,1 18/19 I,L,V 6 L LEU52: -0.142 5 -0.697, 0.404 7,4 18/19 F,I,L,Y 7 E GLU53: 1.061 2* 0.108, 1.367 5,1 18/19 A,E,I,K,Q,S,W 8 E GLU54: 0.909 2* 0.108, 1.367 5,1 18/19 A,E,Q,S 9 G GLY55: -0.349 6 -0.852, 0.108 7,5 18/19 D,E,G,P 10 Q GLN56: -0.600 7 -0.998,-0.344 8,6 18/19 D,E,Q,S 11 G GLY57: 2.391 1 2.816, 2.816 1,1 18/19 E,G,I,K,L,P,S,T,V 12 S SER58: 0.521 4* -0.136, 1.367 5,1 18/19 A,L,M,N,S,T 13 A ALA59: 2.175 1 1.367, 2.816 1,1 18/19 A,D,K,N,R,S,T 14 H HIS60: -0.278 6 -0.852, 0.108 7,5 18/19 F,H,K,S 15 L LEU61: 1.898 1 0.790, 2.816 3,1 18/19 C,F,I,L,V,Y 16 F PHE62: 0.468 4 -0.136, 0.790 5,3 18/19 A,F,L,S,Y 17 T THR63: 0.156 5* -0.529, 0.790 7,3 18/19 A,N,Q,S,T,V 18 V VAL64: -0.901 8 -1.277,-0.697 9,7 18/19 I,L,V 19 L LEU65: 0.975 2* 0.108, 1.367 5,1 18/19 A,I,L,M,R,S,V 20 S SER66: -0.045 5 -0.697, 0.404 7,4 18/19 E,H,R,S,T 21 G GLY67: -1.418 9 -1.755,-1.277 9,9 18/19 G 22 L LEU68: 0.334 4 -0.344, 0.790 6,3 18/19 A,I,K,L,T,V 23 G GLY69: 0.572 3* -0.136, 1.367 5,1 18/19 A,G,I,L,M,V 24 I ILE70: -0.318 6 -0.852, 0.108 7,5 18/19 I,K,R,T 25 R ARG71: 0.405 4 -0.344, 0.790 6,3 18/19 I,L,R,S,T 26 S SER72: -0.248 6 -0.852, 0.108 7,5 18/19 C,S,T,Y 27 T THR73: -0.039 5 -0.529, 0.404 7,4 18/19 K,Q,R,T 28 M MET74: -0.296 6 -0.852, 0.108 7,5 19/19 I,L,M,T,V 29 L LEU75: -0.075 5 -0.529, 0.404 7,4 19/19 A,L,M,S,T 30 E GLU76: 0.959 2* 0.108, 1.367 5,1 19/19 E,G,P,S,T 31 N ASN77: 0.131 5 -0.344, 0.404 6,4 19/19 D,E,N,Q,S,T 32 G GLY78: -1.441 9 -1.755,-1.277 9,9 19/19 G 33 R ARG79: -0.815 7 -1.139,-0.529 8,7 19/19 D,E,K,R 34 R ARG80: -0.887 8 -1.277,-0.529 9,7 19/19 E,Q,R 35 Q GLN81: -1.577 9 -1.755,-1.417 9,9 19/19 Q 36 V VAL82: -0.767 7 -1.139,-0.529 8,7 19/19 I,L,M,V 37 I ILE83: -0.369 6 -0.852, 0.108 7,5 19/19 E,I,L,T,V 38 N ASN84: 0.834 3* 0.108, 1.367 5,1 19/19 A,G,N,R,S 39 F PHE85: -0.749 7 -1.139,-0.344 8,6 19/19 F,L,V 40 L LEU86: 0.791 3* 0.108, 1.367 5,1 19/19 A,C,D,H,L,Q 41 F PHE87: -0.246 6 -0.852, 0.108 7,5 19/19 F,G,L 42 P PRO88: -0.534 7 -0.998,-0.136 8,5 19/19 A,P,V 43 G GLY89: -0.907 8 -1.277,-0.697 9,7 19/19 G,P,S 44 D ASP90: -1.388 9 -1.567,-1.277 9,9 19/19 D,E 45 F PHE91: 0.303 4 -0.344, 0.790 6,3 19/19 A,F,L,M,V,Y 46 I ILE92: -0.023 5 -0.697, 0.404 7,4 19/19 E,F,I,L,V 47 G GLY93: -1.441 9 -1.755,-1.277 9,9 19/19 G 48 L LEU94: 0.935 2* 0.108, 1.367 5,1 19/19 E,F,L,M,R,W 49 Q GLN95: 0.552 3* -0.136, 1.367 5,1 19/19 A,D,E,N,P,Q 50 A ALA96: -0.391 6 -1.139, 0.108 8,5 13/19 A,G 51 G GLY97: 0.022 5 -0.697, 0.404 7,4 13/19 G,I,L 52 L LEU98: 2.561 1 2.816, 2.816 1,1 19/19 A,F,G,H,L,M,P,S,T 53 A ALA99: 2.362 1 1.367, 2.816 1,1 19/19 A,G,N,Q,R,S,T,V 54 G GLY100: 2.565 1 2.816, 2.816 1,1 19/19 D,E,G,I,L,M,N,Q,R,S 55 E GLU101: 1.976 1 1.367, 2.816 1,1 19/19 A,E,H,K,N,Q,R,S,T 56 M MET102: 0.254 4 -0.344, 0.790 6,3 19/19 H,M,N,S,V,Y 57 R ARG103: 1.111 2 0.404, 1.367 4,1 19/19 A,N,P,Q,R,S,T,V 58 H HIS104: 0.562 3* -0.136, 1.367 5,1 19/19 F,G,H,L,N,S,Y 59 S SER105: -0.561 7 -0.998,-0.136 8,5 19/19 D,F,S,Y 60 V VAL106: -1.054 8 -1.417,-0.852 9,7 19/19 A,T,V 61 E GLU107: -0.753 7 -1.139,-0.529 8,7 19/19 D,E,Q,T 62 S SER108: -1.062 8 -1.417,-0.852 9,7 19/19 A,S,T 63 T THR109: -0.040 5 -0.529, 0.404 7,4 19/19 A,I,L,T,V 64 T THR110: -0.845 7 -1.277,-0.529 9,7 19/19 E,G,S,T 65 T THR111: 0.081 5* -0.529, 0.790 7,3 19/19 A,D,E,G,T 66 M MET112: 0.816 3* 0.108, 1.367 5,1 19/19 A,C,L,M,S,T,V 67 V VAL113: 0.008 5 -0.529, 0.404 7,4 19/19 E,L,M,R,T,V 68 L LEU114: -0.103 5 -0.697, 0.404 7,4 19/19 I,L,M,V 69 C CYS115: -0.836 7 -1.277,-0.529 9,7 19/19 A,C,V 70 V VAL116: 2.036 1 1.367, 2.816 1,1 19/19 C,E,I,K,Q,R,T,V 71 F PHE117: -0.769 7 -1.277,-0.344 9,6 19/19 F,I,V 72 N ASN118: 1.494 1 0.790, 2.816 3,1 19/19 A,F,G,K,N,P,R,S 73 R ARG119: -0.223 6 -0.697, 0.108 7,5 19/19 A,F,K,R,Y 74 A ALA120: 1.689 1 0.790, 2.816 3,1 18/19 A,D,E,G,K,N,S,T 75 D ASP121: 1.492 1 0.790, 2.816 3,1 18/19 D,I,L,P,T,V 76 L LEU122: -0.309 6 -0.852, 0.108 7,5 18/19 F,L 77 W TRP123: 1.635 1 0.790, 2.816 3,1 18/19 D,E,F,G,L,Q,W 78 D ASP124: 0.991 2* 0.108, 1.367 5,1 18/19 A,D,E,Q,R 79 L LEU125: -0.503 6 -0.998,-0.136 8,5 18/19 F,L,M,R 80 F PHE126: 0.962 2* 0.108, 1.367 5,1 18/19 A,F,I,L,M,S 81 R ARG127: 1.061 2* 0.108, 1.367 5,1 19/19 E,G,L,Q,R,S 82 E GLU128: 0.612 3* -0.136, 1.367 5,1 19/19 E,K,N,S,T 83 E GLU129: 0.413 4 -0.344, 0.790 6,3 19/19 D,E,M,Q,R,T 84 P PRO130: -1.243 9 -1.567,-0.998 9,8 19/19 P,Q 85 E GLU131: -0.080 5 -0.697, 0.404 7,4 19/19 E,H,K,N,Q 86 R ARG132: 0.801 3* 0.108, 1.367 5,1 19/19 I,L,M,R,V 87 A ALA133: 0.460 4 -0.344, 0.790 6,3 19/19 A,G,L,Q,R,S 88 Y TYR134: 0.879 2* 0.108, 1.367 5,1 19/19 C,H,L,Q,R,Y 89 D ASP135: 0.376 4 -0.344, 0.790 6,3 19/19 A,D,E,Q,R,S 90 L LEU136: -0.372 6 -0.852, 0.108 7,5 19/19 I,L,M 91 T THR137: 0.789 3* 0.108, 1.367 5,1 19/19 H,L,M,N,T,W 92 W TRP138: 0.918 2* 0.108, 1.367 5,1 19/19 A,D,E,R,T,W 93 I ILE139: 0.435 4 -0.344, 0.790 6,3 19/19 E,F,I,L,M,Q 94 A ALA140: -0.562 7 -0.998,-0.136 8,5 19/19 A,M,N,S,T 95 A ALA141: 0.604 3* -0.136, 1.367 5,1 19/19 A,F,I,L,S,T 96 V VAL142: 1.537 1 0.790, 2.816 3,1 19/19 A,D,G,K,N,R,S,T,V 97 E GLU143: -1.054 8 -1.417,-0.852 9,7 19/19 E,G,K 98 E GLU144: -0.200 6 -0.697, 0.108 7,5 19/19 E,I,L,M 99 H HIS145: 0.536 3* -0.136, 1.367 5,1 19/19 A,D,H,K,M,Q,S 100 F PHE146: 1.103 2* 0.108, 2.816 5,1 19/19 A,F,G,L,N,Q,R,S 101 L LEU147: -0.661 7 -1.139,-0.344 8,6 19/19 A,D,L 102 G GLY148: -0.441 6 -0.852,-0.136 7,5 19/19 E,G,Q,R 103 E GLU149: -0.539 7 -0.998,-0.136 8,5 19/19 D,E,K,Q 104 T THR150: 0.063 5 -0.529, 0.404 7,4 19/19 H,M,Q,T,W 105 I ILE151: -0.555 7 -0.998,-0.136 8,5 19/19 A,I,L,M 106 A ALA152: -0.041 5 -0.697, 0.404 7,4 19/19 A,G,L,V 107 S SER153: 0.364 4 -0.344, 0.790 6,3 19/19 L,S,T,V,Y 108 L LEU154: -1.173 8 -1.567,-0.998 9,8 19/19 I,L 109 G GLY155: -1.243 9 -1.567,-0.998 9,8 19/19 G,S 110 Q GLN156: -0.805 7 -1.139,-0.529 8,7 19/19 K,N,Q,R 111 R ARG157: 0.138 5 -0.344, 0.404 6,4 19/19 D,K,M,Q,R 112 D ASP158: -0.224 6 -0.697, 0.108 7,5 19/19 C,D,N,S,T 113 A ALA159: -1.362 9 -1.567,-1.139 9,8 19/19 A,I 114 T THR160: 0.916 2* 0.108, 1.367 5,1 19/19 D,E,N,Q,R,T,V 115 E GLU161: -1.294 9 -1.567,-1.139 9,8 19/19 E,V 116 R ARG162: -0.855 7 -1.277,-0.529 9,7 19/19 K,R 117 L LEU163: -0.418 6 -0.852,-0.136 7,5 19/19 I,L,V 118 A ALA164: -1.261 9 -1.567,-1.139 9,8 19/19 A,G,T 119 W TRP165: -0.387 6 -0.852,-0.136 7,5 19/19 A,H,S,W 120 A ALA166: -0.327 6 -0.852, 0.108 7,5 19/19 A,F,L,Y 121 L LEU167: -0.623 7 -1.139,-0.344 8,6 19/19 I,L 122 L LEU168: 2.061 1 1.367, 2.816 1,1 19/19 A,H,L,S,V,Y 123 R ARG169: 0.245 4 -0.344, 0.790 6,3 19/19 D,G,I,L,N,R 124 I ILE170: -0.525 6 -0.998,-0.136 8,5 19/19 I,L,W 125 H HIS171: 0.296 4 -0.344, 0.790 6,3 19/19 A,C,H,R,S 126 E GLU172: 2.674 1 2.816, 2.816 1,1 19/19 C,D,E,H,K,N,Q,R,T 127 R ARG173: -1.085 8 -1.417,-0.852 9,7 19/19 A,H,R 128 L LEU174: 1.821 1 0.790, 2.816 3,1 19/19 A,D,F,L,Q,S,Y 129 S SER175: 1.545 1 0.790, 2.816 3,1 19/19 A,E,G,L,S 130 A ALA176: 0.878 2* -0.136, 1.367 5,1 19/19 A,G,N,P,Q,R,T 131 I ILE177: 1.408 1 0.404, 2.816 4,1 17/19 E,I,K,P,Q,R,T 132 G GLY178: -0.288 6 -0.852, 0.108 7,5 17/19 G,N,S,T 133 L LEU179: 0.548 3* -0.344, 1.367 6,1 17/19 A,F,L,N,V 134 A ALA180: -0.547 7 -0.998,-0.136 8,5 17/19 A,G,S,T 135 E GLU181: 1.841 1 0.790, 2.816 3,1 18/19 A,D,E,G,H,K,P,S 136 R ARG182: 0.783 3* -0.136, 1.367 5,1 17/19 D,K,M,R,T,V 137 G GLY183: 0.172 5* -0.697, 0.790 7,3 2/19 G,T 138 R ARG184: 0.226 4* -0.529, 0.790 7,3 19/19 A,E,Q,R,T 139 V VAL185: -0.496 6 -1.139,-0.136 8,5 19/19 F,L,V 140 P PRO186: 0.687 3* -0.136, 1.367 5,1 19/19 D,P,R,S,T 141 M MET187: -0.889 8 -1.277,-0.529 9,7 19/19 L,M,V 142 P PRO188: -0.993 8 -1.417,-0.697 9,7 19/19 A,P,T 143 W TRP189: -1.104 8 -1.417,-0.852 9,7 19/19 L,M,W 144 R ARG190: -0.591 7 -0.998,-0.344 8,6 19/19 A,G,R,S,T 145 Q GLN191: -1.107 8 -1.417,-0.852 9,7 19/19 Q,R,W 146 Q GLN192: -0.300 6 -0.852, 0.108 7,5 19/19 A,E,G,Q,T 147 D ASP193: -0.990 8 -1.277,-0.697 9,7 19/19 D,E,Q 148 L LEU194: -0.925 8 -1.277,-0.697 9,7 19/19 I,L,M 149 A ALA195: -1.427 9 -1.755,-1.277 9,9 19/19 A,G 150 D ASP196: -1.403 9 -1.567,-1.277 9,9 19/19 D,N 151 A ALA197: 0.072 5 -0.529, 0.404 7,4 19/19 A,F,Y 152 L LEU198: -1.443 9 -1.755,-1.277 9,9 19/19 L 153 G GLY199: -1.441 9 -1.755,-1.277 9,9 19/19 G 154 L LEU200: -1.044 8 -1.417,-0.697 9,7 19/19 L,T 155 S SER201: -1.493 9 -1.755,-1.417 9,9 19/19 S,T 156 L LEU202: -0.226 6 -0.697, 0.108 7,5 19/19 I,L,P,V 157 V VAL203: -1.296 9 -1.567,-1.139 9,8 19/19 E,V 158 H HIS204: -1.435 9 -1.755,-1.277 9,9 19/19 H,T 159 T THR205: -1.190 8 -1.417,-0.998 9,8 19/19 I,T,V 160 N ASN206: -1.519 9 -1.755,-1.417 9,9 19/19 N,S 161 K LYS207: -1.390 9 -1.567,-1.277 9,9 19/19 K,R 162 T THR208: -0.802 7 -1.277,-0.529 9,7 19/19 L,Q,T,V 163 I ILE209: 0.127 5* -0.529, 0.790 7,3 19/19 F,I,L,M,V 164 R ARG210: -0.459 6 -0.852,-0.136 7,5 19/19 G,K,R,S,T 165 R ARG211: -0.501 6 -0.998,-0.136 8,5 19/19 A,K,R,Y 166 L LEU212: -0.866 7 -1.277,-0.529 9,7 19/19 F,L 167 R ARG213: 0.305 4 -0.344, 0.790 6,3 18/19 A,E,K,Q,R 168 E GLU214: -0.134 5 -0.697, 0.404 7,4 18/19 E,K,R 169 T THR215: 1.641 1 0.790, 2.816 3,1 16/19 D,H,I,L,M,Q,S,T 170 G GLY216: -1.323 9 -1.755,-1.139 9,8 14/19 G 171 H HIS217: 0.687 3* -0.136, 1.367 5,1 4/19 A,H,M,V 172 A ALA218: -0.749 7* -1.277,-0.344 9,6 4/19 A,I 173 L LEU219: -0.200 6* -0.852, 0.404 7,4 4/19 A,L,T 174 W TRP220: 0.478 4* -0.344, 1.367 6,1 4/19 I,L,V,W 175 E GLU221: 0.163 5* -0.697, 0.790 7,3 4/19 E,I,Q 176 G GLY222: -0.526 7* -1.139,-0.136 8,5 4/19 G,H 177 G GLY223: -0.842 7* -1.417,-0.529 9,7 2/19 G 178 T THR224: 0.181 4* -0.697, 0.790 7,3 2/19 G,T 179 L LEU225: -0.327 6* -1.139, 0.404 8,4 1/19 L 180 F PHE226: -0.327 6* -1.139, 0.404 8,4 1/19 F 181 V VAL227: -0.327 6* -1.139, 0.404 8,4 1/19 V
ReferencesReferences
- Spiro, S. 1994. The FNR family of transcriptional regulators. Antonie van Leeuwenhoek 66:23–36.
- PredictProtein: B Rost, G Yachdav and J Liu (2004). The PredictProtein Server. Nucleic Acids Research 32(Web Server issue):W321-W326.